Monitoring changes in the prevalence of the Beijing lineage of Mycobacterium tuberculosis in Ecuador: 2018 and 2023

Background The Mycobacterium tuberculosis Beijing sublineage (Lineage 2) is a major global health concern due to its association with increased transmissibility, hypervirulence, and multidrug resistance (MDR). Although it is dominant in East Asia, its prevalence in South America is generally low, except in some locations in Peru and Colombia, where local prevalences reach up to 16.4 and 15.6%, respectively. Previous studies in Ecuador have reported a very low prevalence (0.43–1.6%), suggesting a lack of active transmission clusters. This study aims to update the molecular epidemiology of the Beijing sublineage in Ecuador by analyzing recent isolates from 2018 and 2023. Methods We analyzed 699 clinical M. tuberculosis isolates collected in 2018 and 2023 using stepwise genotyping. We first screened isolates by allele-specific SNP-PCR targeting the Rv2154724 (G526A) marker, then confirmed results with 24-locus MIRU-VNTR and spoligotyping. We conducted whole-genome sequencing (WGS) on the Beijing-positive isolate to refine lineage assignment and drug-resistance profiling. We assessed genetic relatedness through Minimum Spanning Tree (MST) analysis, incorporating all 12 previously reported M. tuberculosis Beijing isolates in Ecuador. Results Only one isolate from the 384 strains from 2018 (0.26%) was identified as belonging to the M. tuberculosis Beijing sublineage, while no Beijing isolate was detected among the 315 strains from 2023 by SNP-PCR screening. This isolate, collected in 2018 from Machala (El Oro province), was confirmed as Beijing by SNP-PCR and MIRU-24 and additionally as sublineage 2.2.1 by WGS. MST analysis revealed moderate genetic diversity and no active transmission clusters or temporal groupings among Ecuadorian Beijing strains. The identified M. tuberculosis Beijing isolate exhibited a genotypically predicted MDR profile with resistance to rifampicin, isoniazid, ethambutol, and streptomycin. Conclusion The M. tuberculosis Beijing sublineage remains ultra-low in prevalence in Ecuador, with no evidence of consolidated community transmission, even in high-risk border regions. These findings challenge the global consensus on the hyper-adaptability of Beijing strains in South America. Furthermore, our results underscore the limitations of spoligotyping and highlight the need to strengthen and expand genomic surveillance (including WGS) to accurately monitor high-risk M. tuberculosis lineages.